Patch for picard_AddOrReplaceReadGroups.xml to add --tmpdir "${__new_file_path__}" to the command line generated. That will over-ride the default value "/tmp" for opts.tmpdir in picard_wrapper.py and solve the problem with /tmp filling reported by Matt Shirley.

This commit is contained in:
Ross Lazarus
2012-04-04 06:11:54 +10:00
parent f0bf1c4bd4
commit f71f0ff9d2
@@ -16,6 +16,7 @@
--output-format=$outputFormat
--output=$outFile
-j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/AddOrReplaceReadGroups.jar"
--tmpdir "${__new_file_path__}"
</command>
<inputs>
<param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to add or replace read groups in"